Abstract: The crossflow effect significantly affects the three-dimensional boundary layer transition process of hypersonic vehicle. Deepening the understanding of the flow mechanism is helpful to improve the aerodynamic performance and thermodynamic environment of hypersonic vehicle. Aiming at the flow around HIFiRE5 elliptic cone, the characteristics of cross-flow transition in supersonic boundary layer were calculated and analyzed by using large eddy simulation method, and the flow mechanism was revealed. Referring to the HIFiRE5 model test conditions of wind tunnel, in the numerical simulation, an artificial velocity disturbance was applied at the inlet of the elliptic cone to excite the unstable disturbance wave in the boundary layer, and then the basic flow characteristics such as crossflow instability and transition in the hypersonic boundary layer were predicted. Based on the comparison of transition heat flow distribution, it was proved that the calculation results were basically consistent with the experimental data. It is found that the streamwise vortex structure formed by the flow convergence on the center line of the elliptic cone is very easy to become unstable. In addition, there is a strong crossflow instability in the middle region between the center line and the side edge. The two mechanisms affect the boundary layer transition together. Furthermore, the influence of the amplitude of the inflow disturbance on the crossflow instability transition in the boundary layer was analyzed. It is found that under the quiet inflow condition, two groups of independent steady crossflow vortex structures appear in the crossflow region, while under the noisy inflow condition, the instability transition occurs in the main vortex of the centerline and the middle crossflow vortex, and a multi-peak transition front is formed on the surface of the elliptic cone. Finally, the dynamic characteristics of pressure fluctuation in the flow field were deeply analyzed, and the nonlinear evolution mechanism of instability transition in three-dimensional boundary layer was revealed.